1. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Living things abide by chemical laws Chemistry abides by physical laws These rules govern how living things work Physics = forces in/placed on the body (kinesiology, sports medicine, blood pressure, nerve conduction, etc.) Chemistry = how the processes/uses matter (physiology, pharmacy, anesthesia, growth and repair, etc.) Chapter 2: The Chemical Context of Life

2. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Outline: 1)The chemical makeup of life 1)Matter, elements and compounds 2)Atoms and their structure 3)Radioactive isotopes of elements 2)Electrons – what make elements able to bind to and react with each other 1)Electron shells and orbitals 3)Formation of molecules and compounds from elements 1)Covalent Bonds 2)Ionic Bonds 3)Weak chemical bonds (hydrogen bonds, van der Waals interactions) 4)Molecular shape and function

3. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Matter consists of chemical elements in pure form and in combinations called compounds Organisms are composed of matter Matter - anything that takes up space and has mass Matter is made up of elements An element is a substance that cannot be broken down to other substances by chemical reactions A compound is a substance consisting of two or more elements in a fixed ratio

4. SodiumChlorineSodium chloride Which of these are matter? elements? compounds?

5. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Essential Elements of Life About 25 of the 92 naturally occurring elements are essential for life Carbon, hydrogen, oxygen, and nitrogen make up 96% of living matter Most of the remaining 4% consists of calcium, phosphorus, potassium, and sulfur Trace elements are those required by an organism in minute quantities

6. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Deficiencies of different types of elements (a) Nitrogen deficiency (b) Iodine deficiency

7. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings An element’s properties depend on the structure of its atoms Each element consists of unique atoms An atom is the smallest unit of matter that still retains the properties of an element Atoms are composed of subatomic particles Relevant subatomic particles include: – Neutrons (no electrical charge) – Protons (positive charge) – Electrons (negative charge) Neutrons and protons form the atomic nucleus Electrons form a cloud around the nucleus

8. Nucleus Electrons Cloud of negative charge (2 electrons) Simplified views of a Helium atom

9. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Atomic Number and Atomic Mass Atoms of the various elements differ in the number of subatomic particles contained within the core atom structure An element’s atomic number is the number of protons present in one atom An element’s mass number is the sum of protons plus neutrons in the nucleus of one atom Atomic mass, the atom’s total mass, can be approximated by the mass number

10. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Isotopes Atoms of an element ALWAYS have the same number of protons but may differ in number of neutrons. If an atom of a specific element loses or gains a proton, that atom is transformed into an atom of a different element. Isotopes are two atoms of an element that differ in number of neutrons. Remember, they MUST have the same number of protons. Most isotopes are stable, but some are radioactive, giving off particles and energy. When these isotopes undergo radioactive decay, they lose different particles, depending on the type of radioactive decay, and the atoms are often changed into a different element.

11. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Most of the time, we think of radiation as a bad thing (carcinogenic) What good are isotopes in biology? Isotopes

12. Cancerous throat tissue Radioactivity can be used to locate tumors in the body

13. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Energy Levels of Electrons Energy is the capacity to cause some kind of change Potential energy is the energy that matter has because of its location or structure. It is simply the stored energy present in a system that can be used to accomplish something. The electrons of an atom differ in their amounts of potential energy An electron’s state of potential energy is called its energy level A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons. Electrons, like the ball, can only stop on a step of energy, not between steps, just like a ball.

14. Third energy level (shell) Second energy level (shell) First energy level (shell) Atomic nucleus Energy absorbed Energy lost Representation of the energy gained or lost by an electron when it moves between two different energy levels.

15. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Electron Configuration and Chemical Properties The chemical behavior of an atom is determined by the distribution of its electrons in electron shells The periodic table of the elements shows the electron distribution for each element

16. First shell Hydrogen 1 H Lithium 3 Li Second shell Third shell Sodium 11 Na Beryllium 4 Be Magnesium 12 Mg Boron 5 B Aluminum 12 Al Silicon 14 Si Carbon 6 C Nitrogen 7 N Phosphorus 15 P Oxygen 8 O Sulfur 16 S Chlorine 17 Cl Fluorine 9 F Neon 10 Ne Argon 18 Ar Helium 2 He Atomic number Element symbol Electron-shell diagram Atomic mass 2 He 4.00 Electron shell diagrams are often used to represent the number of electrons in an atom (and therefore the charge)

17. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Valence electrons are those in the outermost shell, or valence shell of an atom. The chemical behavior of an atom is mostly determined by the valence electrons – Often determines charge – Determines bonding What electrons in an atom make the atom of an element able to react with other atoms?

18. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Electron Orbitals An orbital is the three-dimensional space where an electron is found 90% of the time – with each electron shell consisting of a SPECIFIC number of orbitals Electron orbitals Electron-shell diagrams 1s orbital2s orbitalThree 2p orbitals1s, 2s, and 2p orbitals First shell (maximum 2 electrons) Second shell (maximum 8 electrons) Neon, with two filled shells (10 electrons) x z y

19. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings How do two atoms come together to form molecules and compounds? The formation and function of molecules depends on chemical bonding between two atoms Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms These interactions usually result in atoms staying close together, held by attractions called chemical bonds Ionic Bond Covalent Bond

20. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Covalent Bonds A covalent bond is the sharing of a pair of valence electrons by two atoms In a covalent bond, the shared electrons count as part of each atom’s valence shell Two atoms are then joined together by virtue of sharing these two electrons to form a molecule Hydrogen atoms (2 H) Hydrogen molecule (H 2 )

21. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings A molecule consists of two or more atoms held together by covalent bonds A double covalent bond, or double bond, is the sharing of two pairs of valence electrons Covalent bonds can form between atoms of the same element or atoms of different elements What do covalent bonds do?

22. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings A single covalent bond, or single bond, is the sharing of one pair of electrons between two atoms

23. Oxygen (O 2 ) Name (molecular formula) Electron- shell diagram Structural formula Space- filling model A double covalent bond, or double bond, is the sharing of two pairs of electrons between two atoms

24. Covalent bonds can form between atoms of the same element, or from different elements. Methane (CH 4 ) Water (H 2 O) Name (molecular formula) Electron- shell diagram Structural formula Space- filling model

25. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Electronegativity is an atom’s attraction for the electrons in a covalent bond The more electronegative an atom, the more strongly it pulls shared electrons toward itself, thus giving it a slightly more negative charge, while the other atom involved in the bond gains a slight positive charge. In a nonpolar covalent bond, the atoms share the electron equally In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally Covalent bonds can actually give the atoms somewhat of a charge

26. H O H H2OH2O ++ ++ –– The covalent bonds in water are polar covalent bonds.

27. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Ionic Bonds Atoms sometimes strip electrons from their bonding partners An example is the transfer of an electron from sodium to chlorine After the transfer of an electron, both atoms have charges A charged atom (or molecule) is called an ion – An anion is a negatively charged ion – A cation is a positively charged ion An ionic bond is an attraction between an anion and a cation

28. Na Sodium atom (an uncharged atom) Cl Chlorine atom (an uncharged atom) Na + Sodium ion (a cation) Cl – Chlorine ion (an anion) Sodium chloride (NaCl) Compounds formed by ionic bonds are called ionic compounds, or salts Salts, such as sodium chloride (table salt), are often found in nature as crystals Ionic Bonds

29. Na + Cl – What is the molecular structure of a crystal? They are very organized and contain regularly spaced atoms.

30. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Weak Chemical Bonds Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules Weak chemical bonds, such as ionic bonds and hydrogen bonds, are also important Weak chemical bonds reinforce shapes of large molecules and help molecules adhere to each other

31. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Hydrogen Bonds A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom In living cells, the electronegative partners are usually oxygen or nitrogen atoms This attraction will weakly hold the two different atoms together and thus, hold the compound these elements are in loosely together. DNA is held together as a double strand by hydrogen bonds.

32. –– ++ ++ –– ++ ++ ++ Hydrogen bonds hold water molecules together (cohesion) Hydrogen bond –– ++ ++ –– Water (H 2 O) –– –– ++ ++ Hydrogen bond Water (H 2 O) Water (H 2 O)

33. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings van der Waals Interactions Molecules or atoms that are very close together can be attracted by fleeting charge differences These weak attractions are called van der Waals interactions Individually, a van der Waals interaction is VERY weak. Collectively, such interactions can be strong, as between molecules of a gecko’s toe hairs and a wall surface

34. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The shape of a molecule dramatically affects its function A molecule’s shape is determined by the positions of its atoms’ valence orbitals In a covalent bond, the s and p orbitals may hybridize, creating specific molecular shapes Biological molecules recognize and interact with each other with a specificity based on molecular shape Molecules with similar shapes can have similar biological effects

35. Natural endorphin Morphine Carbon Hydrogen Nitrogen Sulfur Oxygen Structures of endorphin and morphine Molecules with similar shapes can have similar biological effects

36. Natural endorphin Morphine Brain cell Endorphin receptors Binding to endorphin receptors Molecules with similar shapes can bind to the same cellular receptor

37. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Chemical reactions make and break chemical bonds Chemical reactions lead to new arrangements of atoms The starting molecules of a chemical reaction are called reactants The final molecules of a chemical reaction are called products ReactantsReactionProducts 2 H 2 OO2O2 2 H 2

38. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Why Does This Matter to Living Things? Get together with a partner Name at least two chemical reactions in your body (in which new compounds are created)